Dr. Fazale Rana of Reasons to Believe takes on a new paper that claims that the evolution can explain the Cambrian explosion.

They linked to this article from NBC News, showing how the paper was popularized.

Excerpt:

The team found that the emergence of many sea creatures during the Cambrian explosion could be explained by an accelerated — but not unrealistic — evolution by way of natural selection, or the process in which organisms change over time due to changes in heritable physical or behavioral traits. (For instance, changes that give an organism a leg up will help it survive to pass down that trait to offspring.) The team focused its study on animals related to arthropods, the group that includes crustaceans and other insects.

“In this study we’ve estimated that rates of both morphological and genetic evolution during the Cambrian explosion were five times faster than today – quite rapid, but perfectly consistent with Darwin’s theory of evolution,” Lee said.

That’s the challenge. If you can’t listen to the entire podcast, then let me say that the problem with the paper is the way that they are measuring the “rate of change”. They are only measuring the rates of change in genes and phenotypic characters. They are not measuring other important requirements for the new body plans, like the network interactions and regulatory elements of the network. Also, they haven’t demonstrated a mechanism for even the rapid change they do measure in the genes and phenotypic characters.

I’d like to make two very general observations here. First, measuring rates of change in existing traits is not the same thing as measuring the rate at which new traits appear.

Second, the rapid appearance of new body traits that occurred during the Cambrian explosion could never have taken place without a host of underlying changes at the genetic level. It is these changes that we need to explain. How do we explain, for instance, the sudden increase in the number of new cell types that occurred during the early Cambrian period? Lee et al. do not even discuss this question in their paper: a search on the phrase “cell type” turns up empty.

[…]In a recent post over at Evolution News and Views, Casey Luskin drew readers’ attention to a new book by paleobtologists Douglas Erwin and James Valentine, entitled, The Cambrian Explosion: The Construction of Animal Biodiversity (Roberts and Company, 2013). The authors, who are recognized authorities in their field, are no friends of Intelligent Design, but they firmly reject the standard neo-Darwinian explanations that have been put forward for the Cambrian explosion. In particular, they take issue with the claim that macroevolution is nothing more than an extrapolation of microevolution.

He then prints a few excerpts from the Erwin and Valentine book.

Here’s one:

Increased genetic and developmental interactions were also critical to the formation of new animal body plans. By the time a branch of advanced sponges gave rise to more complex animals, their genomes comprised genes whose products could interact with regulatory elements in a coordinated network. Network interactions were critical to the spatial and temporal patterning of gene expression, to the formation of new cell types, and to the generation of a hierarchical morphology of tissues and organs. The evolving lineages could begin to adapt to different regions within the rich mosaic of conditions they encountered across the environmental landscape, diverging and specializing to diversify into an array of body forms.

Like Dr. Rana said, the new paper never takes these factors into account.

UD continues:

Reading through the introduction, it is readily apparent that Erwin and Valentine have thought long and hard about the issues relating to the Cambrian explosion, and that they truly appreciate the magnitude of the problem of explaining this seismic event in the history of life. By contrast, the new study by Lee et al. fails to grapple with the deeper issues: its aim is merely to defend Darwinism, and it “succeeds” only by shrinking the problem by focusing on minutiae such as rates of change in genes and phenotypic characters. No wonder, then, that the study’s authors perceive no threat to Darwinian evolution in the Cambrian explosion.

So should we be concerned about this paper? I don’t think so – not until they have a mechanism that can drive the required level of innovation. The paper pushes a naturalistic explanation, and so we are within our rights to ask for a naturalistic mechanism. Even if they had the mechanism, they still aren’t taking into account everything that needs to be explained – like regulatory elements in the coordinated network that Erwin and Valentine mentioned.

UPDATE: Kylie asked me a question that caused me to update this post. She asked me what about Behe’s work that shows that Darwinian mechanisms cannot even account for the NORMAL rate of change? I just want to be clear and say that I don’t think that Darwinian mechanisms can even account for that. What the paper does is assume that Darwinian mechanisms can account for the 1X “rate of change” they see. Then they further assume that evolution is able to do the 5X change rate as well. All they did was measure the amount of change and then assert that it’s not that far off of normal. But I don’t accept that Darwinian mechanisms can even do the normal rate of change, because of Behe’s book on the limits of Darwinian mechanisms to drive change.

Michael Ruse and Fuz Rana square off to debate the question “Are natural processes sufficient to explain the origin and the complexity of the cell?” The debate will be moderated by Craig Hazen. Sponsored by The Well Christian Club at UCR, Come Reason Ministries, and Biola University.

Michael Ruse was careful to note that he is not keen on saying design is not possible. Rather, his claim is that naturalism is the most plausible explanation for the origins of life.

Ruse’s argued that design is implausible. Specifically, he noted that if design is the hypothesis put forward, there are any number of ways that one might consider that hypothesis. Is the designer a natural being within the universe or a supernatural being like God? Is there only one designer, or was there a group of designers (and he notes that a group of designers seems more plausible because automobiles require many designers to bring them about)? Finally, he raised the issue of bad design choices. He asked why, if there were a “hands-on” designer, would that designer not grant immunity to HIV and the like.

Ruse also argued that one can fall into the fallacy of selective attention- if one focuses upon only one example in isolation, then one might come to a conclusion that certain laws/theories may not be correct. But placing these same problems in context shows that they can be explained against “the background of our knowledge.”

Finally, Ruse ended with a number of examples for how problems which were seemingly insoluble were explained by naturalistic means. He also argued that one of the popular arguments for design, the flagellum, has so many different varieties (and is sometimes found to be a vestigial organ), and so cannot be shown to be designed.

Fazale Rana Opening

The problems which must be accounted for within an origins of life model are numerous. One must account for self-replication, the emergence of metabolism, the formation of protocells, the synthesis of prebiotic materials, the formation of life’s building blocks, and more.

Rana then turned to some primary models used by researchers to explain origin of life (hereafter OOL). First, there was the replicator-first model, which was problematic because in order for a molecule to be a self-replicator, it must be a homopolymer. But the complexity of the chemical environment on early earth rendered the generation of a homopolymer on the early earth essentially impossible. Next, the metabolism-first model runs into problem due to the chemical networks which have to be in place for metabolism. But the mineral surfaces proposed for the catalytic systems for these proto-metabolic systems cannot serve as such; Leslie Orgel held that this would have to be a “near miracle” and Rana argues that it is virtually impossible. Finally, the membrane-first model requires different steps with exacting conditions such that the model is self-defeating.

Rana argued positively that OOL requires an intelligent agent in order to occur. The reason is because the only way that any of these models can be generated is through the work on OOL in a lab. Thus, they can only be shown to be proof-of-principle and the chemistry breaks down when applied to the early earth. The fact that information is found in the cell is another evidence Rana presented for design. The systems found in enzymes with DNA function as, effectively, Turing machines. Moreover, the way that DNA finds and eliminates mistakes is machine-like as well. The fact that the needed component for success in lab experiments was intelligence hinted, according to Rana, at positive evidence for design.

Finally, Rana argued that due to the “fundamental intractable problems” with naturalistic models for the OOL and the fact that the conditions needed for the OOL and the processes required to bring it about have only been demonstrated as in-principle possible with intelligent agents manipulating the process.

He’s got a summary of each of the speeches, and it rings true with what I saw when I watched the debate.

Michael Ruse and Fuz Rana square off to debate the question “Are natural processes sufficient to explain the origin and the complexity of the cell?” The debate will be moderated by Craig Hazen. Sponsored by The Well Christian Club at UCR, Come Reason Ministries, and Biola University.

Life as we know it on Earth consists of carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHONPS). But could other elements constitute life as we don’t know it?

Not merely a discussion topic for science-fiction buffs, this question bears on origin-of-life discussions and on the search for extraterrestrial life. Carbon-based life requires a strict set of conditions. But perhaps life based on an element like silicon can exist under more extreme conditions. Few places in our solar system, and presumably beyond, can conceivably support carbon-based life. But for life built upon silicon, habitable sites may well abound throughout the universe.

However, of the 112 known chemical elements, only carbon possesses sufficiently complex chemical behavior to sustain living systems. Carbon readily assembles into stable molecules comprised of individual and fused rings and linear and branched chains. It forms single, double, and triple bonds. Carbon also strongly bonds with itself as well as with oxygen, nitrogen, sulfur, and hydrogen.

Carbon serves as the hub of complex molecules. You can join lots of different things to it so that they stay put. But the bonds are not so strong that you can’t break things apart if you really want to. That’s what makes it suitable for making complex life, and why people talk about “carbon-based life”.

The rest of the article explains why other kinds of elements like silicon and phosphorus are not suitable for creating life.

Is carbon synthesis fine-tuned?

Here’s an article by agnostic physicist Paul Davies explaining why people think that the production of carbon in the universe is an example of fine-tuning.

Excerpt:

One of the best-known examples of this life-friendly ‘fine-tuning’ of the laws of physics concerns carbon, the element on which all known life is based. The Big Bang that kicked off the universe coughed out plenty of hydrogen and helium, but no carbon. So where did the carbon in our bodies come from? The answer was worked out in the 1950s: most of the chemical elements heavier than helium were manufactured in the cores of stars, as the product of nuclear fusion reactions. It is the energy released by these reactions that makes the Sun and stars shine.

However, while the details of stellar nuclear reactions are fairly straightforward, there is a notable exception: carbon. Most nuclear reactions in stars occur when two atomic nuclei, rushing around at tremendous speed care of the searing temperatures, collide and fuse, forming a heavier element. But carbon cannot be made this way because all the intermediate steps from helium to carbon involve highly unstable nuclei. The solution, spotted by University of Cambridge astronomer Fred Hoyle, is for carbon to form from the simultaneous collision of three helium nuclei.

THERE IS, HOWEVER, a snag. The chances that three helium nuclei will come together at the same moment are tiny. So Hoyle reasoned that a special factor must be at work to boost the rare reaction and lead to our abundance of carbon. If not, then life in general, and Fred Hoyle in particular, would not exist!

Hoyle knew that nuclear reactions can sometimes be greatly amplified by the phenomenon of resonance, similar to the way that an opera singer can shatter a glass by hitting a certain pitch. Carbon nuclei can resonate too, if the masses and energies of the colliding particles that go to form it are just right. Hoyle worked backwards — he knew the particle masses and energies, and he used them to predict the existence of a carbon resonance.

He then pestered Willy Fowler, a nuclear physicist at the California Institute of Technology, to do an experiment to test the prediction. And sure enough, Hoyle was right. Carbon has a resonant state at exactly the right energy to enable stars to manufacture abundant carbon, and thereby seed the universe with this life-encouraging substance.

Hoyle immediately realised just what a close-run thing this mechanism is. Like Baby Bear’s porridge in the story of Goldilocks, the energy of the carbon resonance has to be “just right”. Too high or too low, and the consequences for life would be catastrophic.

So what determines the carbon resonance? Ultimately it depends on the strength of the force that binds protons and neutrons together in the nucleus. That force is one of the unexplained parameters of basic physics — one of the knobs on the Designer Machine if you like. If the strength of the force that determined the carbon resonance was only a fraction stronger or weaker, it is doubtful there would be observers in the universe to worry about the distinct absence of carbon.

Hoyle himself was deeply impressed by this discovery. “It looks like a put-up job,” he quipped. “A commonsense interpretation of the facts suggests that a superintellect has monkeyed with physics,” he later wrote. A similar conclusion was reached by the Princeton physicist Freeman Dyson: “In some sense, the universe knew we were coming.”

He doesn’t accept that God is the fine-tuner though, so the article just concludes with “it could be” speculations, which is all that naturalists can offer against the standard theistic arguments. Still, what he said about the finely-tuned synthesis of carbon is accurate.